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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-16, 10:56 based on data in: /home/chengxin/pmultiqctest/test_iso/results


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 2/2 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML11
        1|2|3|4|5|6
        1|2|3|4|5|6
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        1|2|3|4|5|6
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_02.mzML21
        1|2|3|4|5|6
        7|8|9|10|11|12
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        7|8|9|10|11|12

        HeatMap

        This plot shows the pipeline performance overview

        This plot shows the pipeline performance overview. Some metrics are calculated.

        • Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
        • Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
        • Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
        • Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
        • Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
        • Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
        • Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
        • Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
        loading..

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 5/5 columns.
        Total MS/MS SpectralTotal MS/MS Spectral IdentifiedIdentified MS/MS Spectral CoverageTotal Peptide IdentifiedTotal Protein IdentifiedTotal Protein Quantified
        12206
        3084
        25.27%
        1183
        488
        488

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 2/2 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML
        1|2|3|4|5|6
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        1
        1214
        1185
        1214
        504
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_02.mzML
        7|8|9|10|11|12
        SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10
        1
        1214
        1185
        1214
        504

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Spectra Tracking

        This plot shows the quantms pipeline mzML tracking

        This table shows the changes in the number of spectra corresponding to each input file during the pipeline operation. And the number of peptides finally identified is obtained from the PSM table in the mzTab file. You can also remove the decoy with the remove_decoy parameter.:

        • MS1_Num: The number of MS1 spectra extracted from mzMLs
        • MS2_Num: The number of MS2 spectra extracted from mzMLs
        • MSGF: The Number of spectra identified by MSGF search engine
        • Comet: The Number of spectra identified by Comet search engine
        • Final result of spectra: extracted from PSM table in mzTab file
        • Final result of Peptides: extracted from PSM table in mzTab file
        Showing 2/2 rows and 6/6 columns.
        Spectra FileMS1_NumMS2_NumFinal result of spectraCometFinal result of PeptidesMSGF
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML
        1431
        6103
        1542
        3309
        1183
        3103
        TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_02.mzML
        1431
        6103
        1542
        3309
        1183
        3103

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Oversampling Distribution

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.

        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.

                    * Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
        
        loading..

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Click distribution to switch to bar plots.
        Showing 50/50 rows and 12/12 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage IntensitySP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5
        1
        ECA3566
        .(TMT6plex)AAAASK(TMT6plex)
        1.00000
        6.82734
        6.82749
        0.00000
        0.00000
        6.82720
        2
        ECA4049
        .(TMT6plex)AADDAK(TMT6plex)
        1.00000
        7.40994
        7.40942
        0.00000
        0.00000
        7.41046
        3
        ECA3787
        .(TMT6plex)AADLGLETVLVER
        1.00000
        6.80568
        6.79577
        0.00000
        0.00000
        6.81559
        4
        ECA3889
        .(TMT6plex)AAFAFPAPIAPVEDDVAALELFHGPTLAFK(TMT6plex)
        1.00000
        4.26944
        4.22324
        0.00000
        0.00000
        4.31564
        5
        ECA1264
        .(TMT6plex)AAGSLVK(TMT6plex)
        0.97875
        6.69699
        6.69146
        0.00000
        0.00000
        6.70252
        6
        ECA3236
        .(TMT6plex)AAIADYK(TMT6plex)
        1.00000
        6.41343
        6.41737
        0.00000
        0.00000
        6.40949
        7
        ECA1363
        .(TMT6plex)AAIDPLVGPQPYQGR
        1.00000
        5.40130
        5.38218
        0.00000
        0.00000
        5.42043
        8
        ECA4012
        .(TMT6plex)AAIEAAGGK(TMT6plex)
        1.00000
        6.82596
        6.82827
        0.00000
        0.00000
        6.82365
        9
        ECA2190
        .(TMT6plex)AAIEALEQELQVLLLPK(TMT6plex)
        1.00000
        4.35127
        4.39664
        0.00000
        0.00000
        4.30590
        10
        ECA2478
        .(TMT6plex)AAIEGNIPLIPGISTVSELMLGMDYGLR
        1.00000
        3.89036
        3.88909
        0.00000
        0.00000
        3.89162
        11
        ECA2439
        .(TMT6plex)AAIEYAITNDR
        1.00000
        6.13298
        6.13273
        0.00000
        0.00000
        6.13324
        12
        ECA3810
        .(TMT6plex)AALEGADMVFIAAGMGGGTGTGAAPVVAEVAK(TMT6plex)
        1.00000
        4.56595
        4.63961
        0.00000
        0.00000
        4.49229
        13
        ECA4007
        .(TMT6plex)AALELAEQR
        1.00000
        6.92690
        6.91393
        0.00000
        0.00000
        6.93987
        14
        ECA0238
        .(TMT6plex)AALESTLAAITESLK(TMT6plex)
        1.00000
        7.39718
        7.39592
        0.00000
        0.00000
        7.39844
        15
        ECA1751
        .(TMT6plex)AALIDC(Methylthio)LAPDR
        1.00000
        6.24059
        6.23503
        0.00000
        0.00000
        6.24615
        16
        ECA3362
        .(TMT6plex)AAMSDVLK(TMT6plex)
        1.00000
        6.64988
        6.65725
        0.00000
        0.00000
        6.64252
        17
        ECA2273
        .(TMT6plex)AANVIGIGINGVDAVSELSK(TMT6plex)
        1.00000
        5.07340
        5.09115
        0.00000
        0.00000
        5.05566
        18
        ECA2496
        .(TMT6plex)AAQDGK(TMT6plex)
        0.99930
        6.10428
        6.10214
        0.00000
        0.00000
        6.10643
        19
        ECA2494
        .(TMT6plex)AAQDSK(TMT6plex)
        0.99930
        6.26613
        6.26694
        0.00000
        0.00000
        6.26532
        20
        ECA4513
        .(TMT6plex)AASFFGSVGGNIVAQVTGMGDNPSVSELIGPVK(TMT6plex)
        1.00000
        3.80306
        3.77783
        0.00000
        0.00000
        3.82830
        21
        ECA1147
        .(TMT6plex)AATAEDR
        1.00000
        4.85120
        4.83680
        0.00000
        0.00000
        4.86559
        22
        ECA4513
        .(TMT6plex)AATDNGGSLIK(TMT6plex)
        0.99269
        6.38062
        6.37315
        0.00000
        0.00000
        6.38808
        23
        ECA4006
        .(TMT6plex)AATILAEQLEAFVDLR
        1.00000
        5.54458
        5.51225
        0.00000
        0.00000
        5.57691
        24
        ECA0402
        .(TMT6plex)AAVLAK(TMT6plex)
        0.99930
        6.54163
        6.52441
        0.00000
        0.00000
        6.55885
        25
        ECA0819
        .(TMT6plex)AAVLESAGINDQSLIEWIK(TMT6plex)
        1.00000
        4.60770
        4.59453
        0.00000
        0.00000
        4.62088
        26
        ECA0871
        .(TMT6plex)AAYAIEDNGAR
        1.00000
        5.45281
        5.44415
        0.00000
        0.00000
        5.46148
        27
        ECA0621
        .(TMT6plex)AC(Methylthio)DEVLNNGK(TMT6plex)
        1.00000
        5.98388
        5.97672
        0.00000
        0.00000
        5.99104
        28
        ECA0685
        .(TMT6plex)AC(Methylthio)IGIITNPVNTTVAIAAEVLK(TMT6plex)
        1.00000
        5.59663
        5.59070
        0.00000
        0.00000
        5.60256
        29
        ECA2831
        .(TMT6plex)ADFNLAGLLPEAVETIEEQAER
        1.00000
        5.62017
        5.62286
        0.00000
        0.00000
        5.61748
        30
        ECA1444
        .(TMT6plex)ADIANLLLAPYFK(TMT6plex)
        1.00000
        6.22742
        6.22114
        0.00000
        0.00000
        6.23371
        31
        ECA4267
        .(TMT6plex)ADISADEVAGIGITNQR
        0.95916
        5.32434
        5.30216
        0.00000
        0.00000
        5.34652
        32
        ECA4281;ECA4290
        .(TMT6plex)ADLLPDSDQQALIAVLDSFVK(TMT6plex)
        1.00000
        4.48215
        4.48365
        0.00000
        0.00000
        4.48065
        33
        ECA4516
        .(TMT6plex)AEAEAER
        1.00000
        5.54297
        5.54016
        0.00000
        0.00000
        5.54577
        34
        ECA1867
        .(TMT6plex)AEAGDVANAIIDGTDAVMLSGESAK(TMT6plex)
        1.00000
        4.75663
        4.72285
        0.00000
        0.00000
        4.79041
        35
        ECA4221
        .(TMT6plex)AEAIAEK(TMT6plex)
        1.00000
        5.59226
        5.58111
        0.00000
        0.00000
        5.60342
        36
        ECA2481
        .(TMT6plex)AEAVC(Methylthio)SDAAMDDIILASDVVMVAR
        1.00000
        4.34160
        4.27324
        0.00000
        0.00000
        4.40996
        37
        ECA3810
        .(TMT6plex)AEEAAEMAISSPLLEDIDLSGAR
        0.99930
        4.89029
        4.87446
        0.00000
        0.00000
        4.90612
        38
        ECA0894
        .(TMT6plex)AEEIVASDPSR
        1.00000
        6.44247
        6.42912
        0.00000
        0.00000
        6.45582
        39
        ECA0224
        .(TMT6plex)AEIIEEAETEVAEIQEQFQSGLVTAGER
        1.00000
        3.79322
        0.00000
        0.00000
        0.00000
        3.79322
        40
        ECA1032
        .(TMT6plex)AEITASLVK(TMT6plex)
        1.00000
        6.81230
        6.80089
        0.00000
        0.00000
        6.82372
        41
        ECA0185
        .(TMT6plex)AELDGK(TMT6plex)
        0.99930
        6.06980
        6.07306
        0.00000
        0.00000
        6.06653
        42
        ECA0385
        .(TMT6plex)AELIDAQVEQLLALAER
        1.00000
        5.77663
        5.76293
        0.00000
        0.00000
        5.79033
        43
        ECA0842
        .(TMT6plex)AEMDIEK(TMT6plex)
        0.99930
        5.79654
        5.80795
        0.00000
        0.00000
        5.78513
        44
        ECA2460
        .(TMT6plex)AEQQAK(TMT6plex)
        1.00000
        6.07244
        6.07312
        0.00000
        0.00000
        6.07176
        45
        ECA0639
        .(TMT6plex)AESALK(TMT6plex)
        0.96895
        5.24474
        5.23655
        0.00000
        0.00000
        5.25293
        46
        ECA1456
        .(TMT6plex)AEVEQAIASAAAAFPAWSK(TMT6plex)
        1.00000
        5.23008
        5.20405
        0.00000
        0.00000
        5.25611
        47
        ECA2481
        .(TMT6plex)AEVMDVANAVLDGTDAVMLSAETAAGQYPAETVAAMAK(TMT6plex)
        1.00000
        4.49932
        4.44221
        0.00000
        0.00000
        4.55643
        48
        ECA0690
        .(TMT6plex)AEVVAHGR
        1.00000
        5.84314
        5.85972
        0.00000
        0.00000
        5.82655
        49
        ECA4426
        .(TMT6plex)AEWDNVTVR
        1.00000
        6.29147
        6.28002
        0.00000
        0.00000
        6.30292
        50
        ECA1853
        .(TMT6plex)AFDFAC(Methylthio)LPNDGVGLAR
        1.00000
        5.59686
        5.57642
        0.00000
        0.00000
        5.61729
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.Click distribution to switch to bar plots.
        Showing 50/50 rows and 10/10 columns.
        ProteinNamePeptides_NumberAverage IntensitySP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5SP=Yeast;CT=protein;AC=P00924;QY=10SP=Yeast;CT=protein;AC=P00924;QY=1SP=Yeast;CT=protein;AC=P00924;QY=5SP=Yeast;CT=protein;AC=P00924;QY=2.5
        ECA0003
        2
        5.84871
        5.84338
        0.00000
        0.00000
        5.85404
        ECA0013
        3
        6.39263
        6.39716
        0.00000
        0.00000
        6.38809
        ECA0029
        5
        6.51292
        6.49321
        0.00000
        0.00000
        6.53262
        ECA0030
        1
        5.36446
        5.35471
        0.00000
        0.00000
        5.37421
        ECA0050
        1
        4.33329
        4.35722
        0.00000
        0.00000
        4.30937
        ECA0055
        5
        6.00726
        5.98869
        0.00000
        0.00000
        6.02584
        ECA0077
        1
        6.97439
        6.97933
        0.00000
        0.00000
        6.96945
        ECA0078
        1
        4.40377
        4.39976
        0.00000
        0.00000
        4.40779
        ECA0085
        1
        3.57998
        3.56467
        0.00000
        0.00000
        3.59530
        ECA0091
        1
        6.01794
        6.02381
        0.00000
        0.00000
        6.01206
        ECA0092
        5
        7.19602
        7.19132
        0.00000
        0.00000
        7.20072
        ECA0094
        1
        4.79712
        4.80797
        0.00000
        0.00000
        4.78627
        ECA0098
        1
        4.58981
        4.56733
        0.00000
        0.00000
        4.61229
        ECA0102
        1
        4.37598
        4.33196
        0.00000
        0.00000
        4.41999
        ECA0104
        4
        6.28885
        6.27274
        0.00000
        0.00000
        6.30496
        ECA0125
        1
        4.96002
        4.93182
        0.00000
        0.00000
        4.98821
        ECA0130
        2
        6.36943
        6.35633
        0.00000
        0.00000
        6.38254
        ECA0146
        1
        5.97282
        5.97191
        0.00000
        0.00000
        5.97374
        ECA0172
        3
        6.93965
        6.93158
        0.00000
        0.00000
        6.94772
        ECA0185
        1
        6.06980
        6.07306
        0.00000
        0.00000
        6.06653
        ECA0193
        1
        5.33499
        5.30491
        0.00000
        0.00000
        5.36507
        ECA0208
        1
        5.99070
        5.95834
        0.00000
        0.00000
        6.02307
        ECA0216;ECA4035
        15
        7.83694
        7.81974
        0.00000
        0.00000
        7.85414
        ECA0219
        2
        7.24991
        7.23194
        0.00000
        0.00000
        7.26788
        ECA0220
        3
        7.20573
        7.20059
        0.00000
        0.00000
        7.21087
        ECA0221
        4
        7.27118
        7.25680
        0.00000
        0.00000
        7.28556
        ECA0222
        5
        7.01649
        7.00828
        0.00000
        0.00000
        7.02470
        ECA0223
        10
        6.39487
        6.37797
        0.00000
        0.00000
        6.41177
        ECA0224
        9
        6.34868
        6.33495
        0.00000
        0.00000
        6.36242
        ECA0238
        2
        7.40436
        7.40282
        0.00000
        0.00000
        7.40590
        ECA0247
        2
        6.30346
        6.28195
        0.00000
        0.00000
        6.32498
        ECA0255
        1
        4.72412
        4.74201
        0.00000
        0.00000
        4.70624
        ECA0260
        1
        4.84006
        4.86407
        0.00000
        0.00000
        4.81605
        ECA0261
        1
        4.87473
        4.85298
        0.00000
        0.00000
        4.89648
        ECA0264
        1
        6.32090
        6.32218
        0.00000
        0.00000
        6.31963
        ECA0265
        2
        5.37448
        5.34624
        0.00000
        0.00000
        5.40272
        ECA0267
        1
        4.80976
        4.78025
        0.00000
        0.00000
        4.83928
        ECA0273
        1
        4.29460
        4.31027
        0.00000
        0.00000
        4.27893
        ECA0281
        1
        3.97171
        3.98894
        0.00000
        0.00000
        3.95448
        ECA0282
        1
        4.38223
        4.32774
        0.00000
        0.00000
        4.43673
        ECA0287
        1
        5.92266
        5.88823
        0.00000
        0.00000
        5.95708
        ECA0293
        1
        4.89779
        4.84757
        0.00000
        0.00000
        4.94800
        ECA0301
        1
        6.08874
        6.07322
        0.00000
        0.00000
        6.10425
        ECA0303
        3
        5.92532
        5.90885
        0.00000
        0.00000
        5.94180
        ECA0306
        2
        6.67854
        6.66231
        0.00000
        0.00000
        6.69477
        ECA0308
        3
        5.49164
        5.48327
        0.00000
        0.00000
        5.50000
        ECA0310
        5
        6.77925
        6.76869
        0.00000
        0.00000
        6.78981
        ECA0316
        1
        4.08222
        4.09415
        0.00000
        0.00000
        4.07029
        ECA0333
        1
        4.53056
        4.51838
        0.00000
        0.00000
        4.54275
        ECA0372
        2
        6.30310
        6.29774
        0.00000
        0.00000
        6.30845
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        CONSENSUSID ConsensusID 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DECOYDATABASE DecoyDatabase 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        EXTRACTPSMFEATURES PSMFeatureExtractor 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FDRCONSENSUSID FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FILEMERGE FileMerger 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDCONFLICTRESOLVER IDConflictResolver 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDMAPPER IDMapper 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        ISOBARICANALYZER IsobaricAnalyzer 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSCONVERTER MSstatsConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSTMT bioconductor-msstatstmt 2.2.0
        r-base 4.1.1
        MZMLINDEXING FileConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PERCOLATOR PercolatorAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        percolator 3.05.0, Build Date Aug 31 2020 19:03:04
        PROTEININFERENCER ProteinInference 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PROTEINQUANTIFIER ProteinQuantifier 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        SEARCHENGINECOMET Comet 2019.01 rev. 5
        CometAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        lethal_rosalind
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_tmt,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/tmt_testdata/PXD000001.sdrf.tsv
        outdir
        ./results_iso
        root_folder
        /home/chengxin/tmt_testdata/

        Protein database

        database
        /home/chengxin/tmt_testdata/erwinia_carotovora.fasta
        add_decoys
        true
        decoy_string
        rev

        Database search

        search_engines
        msgf,comet
        instrument
        N/A
        protocol
        TMT

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein inference

        psm_level_fdr_cutoff
        1.0

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Full test profile DDA ISO
        config_profile_description
        Full test dataset in isotopic labelling mode to check pipeline function and sanity of results

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A